"Batch processing Available from command line. ImageAlpha is based on pngquant. You'll find compiled pngquant executable in ImageAlpha.app/Contents/Resources directory."

So you should be able to script that.

Also for people on non-Mac systems, it appears this is available for Linux / Windows as well: https://github.com/pornel/pngquant

Edit: Better link to pngquant: http://pngquant.org/